# HG changeset patch # User sjung # Date 1494438947 14400 # Node ID 2d6315e241e42c17557ef4edb0c41de8272011d7 Uploaded diff -r 000000000000 -r 2d6315e241e4 Galaxy-Workflow-DNAse-footprints-singlesample-bamInput_wellington_hint_piq.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-DNAse-footprints-singlesample-bamInput_wellington_hint_piq.ga Wed May 10 13:55:47 2017 -0400 @@ -0,0 +1,531 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "DNAse-footprints-singlesample-bamInput_wellington_hint_piq", + "steps": { + "0": { + "annotation": "0", + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "0", + "name": "sorted Bam" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 226.383544921875, + "top": 220.94318389892578 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"sorted Bam\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [], + "uuid": "None" + }, + "1": { + "annotation": "2", + "id": 1, + "input_connections": {}, + "inputs": [], + "label": null, + "name": "Convert from BAM to BED", + "outputs": [ + { + "name": "output", + "type": "bed" + } + ], + "position": { + "left": 466.2727355957031, + "top": 210.88920211791992 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_errors": null, + "tool_id": "bedtools_bamtobed", + "tool_state": "{\"__page__\": 0, \"option\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"input_source\": \"{\\\"input_type\\\": \\\"file\\\", \\\"__current_case__\\\": 1, \\\"input_file\\\": null}\", \"tag\": \"\\\"\\\"\", \"split\": \"\\\"False\\\"\", \"ed_score\": \"\\\"False\\\"\"}", + "tool_version": "BEDTOOLS: 2.17.0", + "type": "tool", + "user_outputs": [], + "uuid": "None" + }, + "2": { + "annotation": "3", + "id": 2, + "input_connections": { + "input": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "piq", + "outputs": [ + { + "name": "output", + "type": "csv" + } + ], + "position": { + "left": 1022.210205078125, + "top": 532.2102203369141 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_errors": null, + "tool_id": "piq", + "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", + "tool_version": "PIQ: 1.3", + "type": "tool", + "user_outputs": [], + "uuid": "None" + }, + "3": { + "annotation": "4", + "id": 3, + "input_connections": { + "fd_0|input": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "FSeq", + "outputs": [ + { + "name": "output", + "type": "bed,wig" + } + ], + "position": { + "left": 513.2613689899445, + "top": 375.875 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_errors": null, + "tool_id": "fseq", + "tool_state": "{\"__page__\": 0, \"outputFormat\": \"\\\"bed\\\"\", \"wiggleTrackStep\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"featLen\": \"\\\"600\\\"\", \"fd\": \"[{\\\"__index__\\\": 0, \\\"input\\\": null}]\", \"threshold\": \"\\\"2.5\\\"\", \"fragSize\": \"\\\"0\\\"\"}", + "tool_version": "F-Seq: 1.85", + "type": "tool", + "user_outputs": [], + "uuid": "None" + }, + "4": { + "annotation": "16", + "id": 4, + "input_connections": { + "input": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Uniq", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 1246.03125, + "top": 541.0170440673828 + }, + "post_job_actions": { + "RenameDatasetActionoutput": { + "action_arguments": { + "newname": "piq_uniq" + }, + "action_type": "RenameDatasetAction", + "output_name": "output" + } + }, + "tool_errors": null, + "tool_id": "uniq", + "tool_state": "{\"columnList\": \"\\\"1,2,3\\\"\", \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [], + "uuid": "7dcb1018-baa2-48a1-a0ee-478d8edced77" + }, + "5": { + "annotation": "6", + "id": 5, + "input_connections": { + "input": { + "id": 3, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Cut", + "outputs": [ + { + "name": "out_file1", + "type": "tabular" + } + ], + "position": { + "left": 389.2841033935547, + "top": 528.8863372802734 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "Cut1", + "tool_state": "{\"columnList\": \"\\\"c1,c2,c3\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", + "tool_version": "1.0.1", + "type": "tool", + "user_outputs": [], + "uuid": "None" + }, + "6": { + "annotation": "8", + "id": 6, + "input_connections": { + "input": { + "id": 5, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Compute", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 587.28125, + "top": 531.8834991455078 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "Add_a_column1", + "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"c2-c3\\\"\", \"round\": \"\\\"no\\\"\", \"__page__\": 0}", + "tool_version": "1.1.0", + "type": "tool", + "user_outputs": [], + "uuid": "None" + }, + "7": { + "annotation": "9", + "id": 7, + "input_connections": { + "input": { + "id": 6, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Filter", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 788.2897644042969, + "top": 531.8834991455078 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "Filter1", + "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"c4<-400\\\"\", \"__page__\": 0}", + "tool_version": "1.1.0", + "type": "tool", + "user_outputs": [], + "uuid": "None" + }, + "8": { + "annotation": "10", + "id": 8, + "input_connections": { + "input": { + "id": 7, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Cut", + "outputs": [ + { + "name": "out_file1", + "type": "tabular" + } + ], + "position": { + "left": 784.7102355957031, + "top": 367.2670440673828 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "Cut1", + "tool_state": "{\"columnList\": \"\\\"c1,c2,c3\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", + "tool_version": "1.0.1", + "type": "tool", + "user_outputs": [], + "uuid": "None" + }, + "9": { + "annotation": "11", + "id": 9, + "input_connections": { + "input": { + "id": 8, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Filter", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 779.8806762695312, + "top": 221.44318389892578 + }, + "post_job_actions": { + "ChangeDatatypeActionout_file1": { + "action_arguments": { + "newtype": "bed" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "out_file1" + }, + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "Filter1", + "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"c1=='chr1' or c1=='chr2'or c1=='chr3' or c1=='chr4' or c1=='chr5' or c1=='chr6' or c1=='chr7' or c1=='chr8' or c1=='chr9' or c1=='chr10' or c1=='chr11' or c1=='chr12' or c1=='chr13' or c1=='chr14' or c1=='chr15' or c1=='chr16' or c1=='chr17' or c1=='chr18' or c1=='chr19' or c1=='chr20' or c1=='chr21' or c1=='chr22' or c1=='chrX' or c1=='chrY'\\\"\", \"__page__\": 0}", + "tool_version": "1.1.0", + "type": "tool", + "user_outputs": [], + "uuid": "None" + }, + "10": { + "annotation": "12", + "id": 10, + "input_connections": { + "bam_file": { + "id": 0, + "output_name": "output" + }, + "bed_file": { + "id": 9, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Wellington Footprints", + "outputs": [ + { + "name": "output", + "type": "bed" + } + ], + "position": { + "left": 984.9090881347656, + "top": 207.96306610107422 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_errors": null, + "tool_id": "wellington_footprints", + "tool_state": "{\"__page__\": 0, \"bam_file\": \"null\", \"bed_file\": \"null\", \"__rerun_remap_job_id__\": null, \"fdrlimit\": \"\\\"0\\\"\"}", + "tool_version": "0.2.5", + "type": "tool", + "user_outputs": [], + "uuid": "None" + }, + "11": { + "annotation": "13", + "id": 11, + "input_connections": { + "input": { + "id": 0, + "output_name": "output" + }, + "region": { + "id": 9, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Hint", + "outputs": [ + { + "name": "output", + "type": "bed" + } + ], + "position": { + "left": 996.897705078125, + "top": 371.9545440673828 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_errors": null, + "tool_id": "hint", + "tool_state": "{\"input\": \"null\", \"region\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", + "tool_version": "HINT: 1.1.1", + "type": "tool", + "user_outputs": [], + "uuid": "None" + }, + "12": { + "annotation": "14", + "id": 12, + "input_connections": { + "input": { + "id": 10, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Sort", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 1225.9176025390625, + "top": 206.9545440673828 + }, + "post_job_actions": { + "RenameDatasetActionout_file1": { + "action_arguments": { + "newname": "wellington_sorted" + }, + "action_type": "RenameDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "sort1", + "tool_state": "{\"__page__\": 0, \"style\": \"\\\"alpha\\\"\", \"column\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"order\": \"\\\"ASC\\\"\", \"input\": \"null\", \"column_set\": \"[]\"}", + "tool_version": "1.0.1", + "type": "tool", + "user_outputs": [], + "uuid": "None" + }, + "13": { + "annotation": "15", + "id": 13, + "input_connections": { + "input": { + "id": 11, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Sort", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 1231.897705078125, + "top": 395.9460144042969 + }, + "post_job_actions": { + "RenameDatasetActionout_file1": { + "action_arguments": { + "newname": "hint_sorted" + }, + "action_type": "RenameDatasetAction", + "output_name": "out_file1" + } + }, + "tool_errors": null, + "tool_id": "sort1", + "tool_state": "{\"__page__\": 0, \"style\": \"\\\"alpha\\\"\", \"column\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"order\": \"\\\"ASC\\\"\", \"input\": \"null\", \"column_set\": \"[]\"}", + "tool_version": "1.0.1", + "type": "tool", + "user_outputs": [], + "uuid": "None" + } + }, + "uuid": "a1168692-fb6d-4143-b956-fe7f10370bec" +} \ No newline at end of file